sdf name problem

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sdf name problem

Postby mai el-naggar » Mon Dec 02, 2013 4:37 pm

I am doing docking using autodock vina, pyrx 0.8, windows. Most of the compounds that I am using in my project for docking are new and they don't have sdf files in pubchem or zinc. so I had to construct these ligands using chemBio 3D ultra 12.0 and saved them as sdf files, the problem is that when I use these files with openbabel, the file name disappear and all the ligands appear with the name fragment, while when I use sdf file for the known compounds downloaded from pubchem,the file name does not change.
It worth noted that there is no problem in the docking process, and I can know the binding energy for each ligand if the results are not arranged, but this will be better if the file name doesn't change, I am using only two letters named files
thanks in advance
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Re: sdf name problem

Postby sargis » Tue Dec 03, 2013 12:54 am

PyRx is using title of the molecule from sdf files as the name of the molecule:
https://sourceforge.net/p/pyrx/code/HEA ... bel.py#l48

You can edit sdf files with your favorite text editor (e.g. notepad/wordpad), replace the first line with the name of the file and save it. Naming ligands after sdf file name makes sense when there is only one molecule in sdf.

Thank you for using PyRx!
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Re: sdf name problem

Postby mai el-naggar » Tue Dec 03, 2013 3:37 pm

Thank you so much
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